package org.cbioportal.legacy.web;

import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.Parameter;
import io.swagger.v3.oas.annotations.media.ArraySchema;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.media.Schema;
import io.swagger.v3.oas.annotations.responses.ApiResponse;
import io.swagger.v3.oas.annotations.tags.Tag;
import jakarta.validation.Valid;
import jakarta.validation.constraints.Max;
import jakarta.validation.constraints.Min;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import org.cbioportal.legacy.model.Patient;
import org.cbioportal.legacy.service.PatientService;
import org.cbioportal.legacy.service.exception.PatientNotFoundException;
import org.cbioportal.legacy.service.exception.StudyNotFoundException;
import org.cbioportal.legacy.web.config.PublicApiTags;
import org.cbioportal.legacy.web.config.annotation.PublicApi;
import org.cbioportal.legacy.web.parameter.Direction;
import org.cbioportal.legacy.web.parameter.HeaderKeyConstants;
import org.cbioportal.legacy.web.parameter.PagingConstants;
import org.cbioportal.legacy.web.parameter.PatientFilter;
import org.cbioportal.legacy.web.parameter.PatientIdentifier;
import org.cbioportal.legacy.web.parameter.Projection;
import org.cbioportal.legacy.web.parameter.sort.PatientSortBy;
import org.cbioportal.legacy.web.util.UniqueKeyExtractor;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.validation.annotation.Validated;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestAttribute;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;

@PublicApi
@RestController()
@RequestMapping("/api")
@Validated
@Tag(name = PublicApiTags.PATIENTS, description = " ")
public class PatientController {

  @Autowired private PatientService patientService;

  @RequestMapping(
      value = "/patients",
      method = RequestMethod.GET,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @Operation(description = "Get all patients")
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content = @Content(array = @ArraySchema(schema = @Schema(implementation = Patient.class))))
  public ResponseEntity<List<Patient>> getAllPatients(
      @Parameter(description = "Search keyword that applies to ID of the patients")
          @RequestParam(required = false)
          String keyword,
      @Parameter(description = "Level of detail of the response")
          @RequestParam(defaultValue = "SUMMARY")
          Projection projection,
      @Parameter(description = "Page size of the result list")
          @Max(PagingConstants.MAX_PAGE_SIZE)
          @Min(PagingConstants.MIN_PAGE_SIZE)
          @RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_SIZE)
          Integer pageSize,
      @Parameter(description = "Page number of the result list")
          @Min(PagingConstants.MIN_PAGE_NUMBER)
          @RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_NUMBER)
          Integer pageNumber,
      @Parameter(description = "Name of the property that the result list is sorted by")
          @RequestParam(required = false)
          PatientSortBy sortBy,
      @Parameter(description = "Direction of the sort") @RequestParam(defaultValue = "ASC")
          Direction direction)
      throws StudyNotFoundException {

    if (projection == Projection.META) {
      HttpHeaders responseHeaders = new HttpHeaders();
      responseHeaders.add(
          HeaderKeyConstants.TOTAL_COUNT,
          patientService.getMetaPatients(keyword).getTotalCount().toString());
      return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
    } else {
      return new ResponseEntity<>(
          patientService.getAllPatients(
              keyword,
              projection.name(),
              pageSize,
              pageNumber,
              sortBy == null ? null : sortBy.getOriginalValue(),
              direction.name()),
          HttpStatus.OK);
    }
  }

  @PreAuthorize(
      "hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
  @RequestMapping(
      value = "/studies/{studyId}/patients",
      method = RequestMethod.GET,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @Operation(description = "Get all patients in a study")
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content = @Content(array = @ArraySchema(schema = @Schema(implementation = Patient.class))))
  public ResponseEntity<List<Patient>> getAllPatientsInStudy(
      @Parameter(required = true, description = "Study ID e.g. acc_tcga") @PathVariable
          String studyId,
      @Parameter(description = "Level of detail of the response")
          @RequestParam(defaultValue = "SUMMARY")
          Projection projection,
      @Parameter(description = "Page size of the result list")
          @Max(PagingConstants.MAX_PAGE_SIZE)
          @Min(PagingConstants.MIN_PAGE_SIZE)
          @RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_SIZE)
          Integer pageSize,
      @Parameter(description = "Page number of the result list")
          @Min(PagingConstants.MIN_PAGE_NUMBER)
          @RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_NUMBER)
          Integer pageNumber,
      @Parameter(description = "Name of the property that the result list is sorted by")
          @RequestParam(required = false)
          PatientSortBy sortBy,
      @Parameter(description = "Direction of the sort") @RequestParam(defaultValue = "ASC")
          Direction direction)
      throws StudyNotFoundException {

    if (projection == Projection.META) {
      HttpHeaders responseHeaders = new HttpHeaders();
      responseHeaders.add(
          HeaderKeyConstants.TOTAL_COUNT,
          patientService.getMetaPatientsInStudy(studyId).getTotalCount().toString());
      return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
    } else {
      return new ResponseEntity<>(
          patientService.getAllPatientsInStudy(
              studyId,
              projection.name(),
              pageSize,
              pageNumber,
              sortBy == null ? null : sortBy.getOriginalValue(),
              direction.name()),
          HttpStatus.OK);
    }
  }

  @PreAuthorize(
      "hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
  @RequestMapping(
      value = "/studies/{studyId}/patients/{patientId}",
      method = RequestMethod.GET,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @Operation(description = "Get a patient in a study")
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content = @Content(schema = @Schema(implementation = Patient.class)))
  public ResponseEntity<Patient> getPatientInStudy(
      @Parameter(required = true, description = "Study ID e.g. acc_tcga") @PathVariable
          String studyId,
      @Parameter(required = true, description = "Patient ID e.g. TCGA-OR-A5J2") @PathVariable
          String patientId)
      throws PatientNotFoundException, StudyNotFoundException {

    return new ResponseEntity<>(
        patientService.getPatientInStudy(studyId, patientId), HttpStatus.OK);
  }

  @PreAuthorize(
      "hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
  @RequestMapping(
      value = "/patients/fetch",
      method = RequestMethod.POST,
      consumes = MediaType.APPLICATION_JSON_VALUE,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content = @Content(array = @ArraySchema(schema = @Schema(implementation = Patient.class))))
  public ResponseEntity<List<Patient>> fetchPatients(
      @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface
          @RequestAttribute(required = false, value = "involvedCancerStudies")
          Collection<String> involvedCancerStudies,
      @Parameter(
              hidden =
                  true) // prevent reference to this attribute in the swagger-ui interface. this
          // attribute is needed for the @PreAuthorize tag above.
          @Valid
          @RequestAttribute(required = false, value = "interceptedPatientFilter")
          PatientFilter interceptedPatientFilter,
      @Parameter(required = true, description = "List of patient identifiers")
          @Valid
          @RequestBody(required = false)
          PatientFilter patientFilter,
      @Parameter(description = "Level of detail of the response")
          @RequestParam(defaultValue = "SUMMARY")
          Projection projection) {

    List<String> studyIds = new ArrayList<>();
    List<String> patientIds = new ArrayList<>();

    if (projection == Projection.META) {
      HttpHeaders responseHeaders = new HttpHeaders();
      if (interceptedPatientFilter.getPatientIdentifiers() != null) {
        extractStudyAndPatientIds(interceptedPatientFilter, studyIds, patientIds);
      } else {
        UniqueKeyExtractor.extractUniqueKeys(
            interceptedPatientFilter.getUniquePatientKeys(), studyIds, patientIds);
      }
      responseHeaders.add(
          HeaderKeyConstants.TOTAL_COUNT,
          patientService.fetchMetaPatients(studyIds, patientIds).getTotalCount().toString());
      return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
    } else {
      if (interceptedPatientFilter.getPatientIdentifiers() != null) {
        extractStudyAndPatientIds(interceptedPatientFilter, studyIds, patientIds);
      } else {
        UniqueKeyExtractor.extractUniqueKeys(
            interceptedPatientFilter.getUniquePatientKeys(), studyIds, patientIds);
      }
      // TODO: since we are already extracting the studyIds in the interceptor, we might not need to
      // use the service here
      return new ResponseEntity<>(
          patientService.fetchPatients(studyIds, patientIds, projection.name()), HttpStatus.OK);
    }
  }

  private void extractStudyAndPatientIds(
      PatientFilter patientFilter, List<String> studyIds, List<String> patientIds) {

    for (PatientIdentifier patientIdentifier : patientFilter.getPatientIdentifiers()) {
      studyIds.add(patientIdentifier.getStudyId());
      patientIds.add(patientIdentifier.getPatientId());
    }
  }
}
